Team:OUC-China
During the experiment, we communicated with Nanjing University（NJU-China） to fully understand each other's projects and conducted in-depth cooperation in the experiment. They had exosome design in their project, so they used exosomes to help us test our transfer RNA, and we helped them solve some modeling problems. Both sides have learned greatly. We also had online communication with team Tianjin. We were interested in their project, so we conducted an online meeting with Team Tianjin. We had a good communication with each other, Tianjin helped us solve some problems in dry lab, and we shared some ideas with them in modeling. Both of us had broadened our thinking and better our design. In July，We worked with JNU-China, FAFU-China, NFU-China，XMU-China and BIT on the art side. Co-produced science comics were used to educate the public about synthetic biology and IGEM. We published the comics on our respective wechat public account platform simultaneously, and made them into paper pamphlets, which were used in later science education and communication. DUT-China is also an important partner of our team. In the initial communication and coding of DNA sequences, we put forward different ideas. The DUT-China team proposed single-hot coding, while the OUC-China team proposed sequential coding and K-MERS processing of sequences. After model processing, we found that K-MERS treatment could not improve model features or accuracy, so we shared this experience in the subsequent communication.
In the mid-stage period, we found that the effect of the model was poor. DUT-China proposed that "physical and chemical properties of sequences can be added to the training set" and told us the required Python library. In the later modeling, we found that the effect of the model was indeed improved to a certain extent. We also work with DUT-China on offline education. On June 27th, 2022, we had a discussion on synthetic biology with DUT-China and NEU-China. Our discussion mainly focused on the following three parts:
Partnership
NJU-China
Tianjin
FAFU-China＆JNU-China＆NEFU-China＆XMU-China＆BIT
DUT-China
When optimizing the model, DUT believes that "in the case of small data sets, neural networks can be abandoned and some weak learners can be used for learning, such as" random forest "; OUC-China provides the method "Using grid search to determine the optimal hyperparameters of weak learner, so as to achieve the best model". The two sides had full exchanges.
We also collaborate with DUT-China in wet experiments. We showed them our new classis Aureobasidium melanogenum P16. DUT-China sent their SacB plasmid to us to test their suicide protein with our new chassis Aureobasidium melanogenum P16 , receiving good results.
As shown in figure 8(on the left), our team has introduced 183bp specific fragment of SacB plasmid into Aureobasidium melanogenum P16
As shown in figure 8(on the right), the area 1 was the one with empty genome transformation plasmid, the area 2 was the one with SacB gene fragment genome transformation plasmid, and the area 3 was the one with 5nM transformation plasmid. We have proved that SacB from DUT-China truly has the toxicity of ontological expression.
1. Understanding of synthetic biology by each team.
2. Links between projects of each team and synthetic biology.
3. How to popularize science of synthetic biology.
The seminar was unexpectedly successful, as everyone expressed their opinions warmly. Through discussion, we optimized our education program and the science popularization. See “Education” for more information.
